Variant report

Variant	rs2479768
Chromosome Location	chr13:29620654-29620655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1358937	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs167834	1.00[GIH][hapmap]
rs1923518	1.00[CEU][hapmap]
rs1927839	1.00[GIH][hapmap]
rs226904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226906	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs226909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs2475527	1.00[GIH][hapmap]
rs2475528	1.00[GIH][hapmap]
rs2475539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475540	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475541	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475543	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475544	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2475547	0.91[EUR][1000 genomes]
rs2479759	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479760	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479766	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479772	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2479783	1.00[GIH][hapmap]
rs2484464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484465	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28434554	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987343	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326510	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326512	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs326516	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs326518	0.96[EUR][1000 genomes]
rs326522	0.91[EUR][1000 genomes]
rs326523	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4238114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768998	0.96[EUR][1000 genomes]
rs4769660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769669	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769671	1.00[CEU][hapmap];0.87[MKK][hapmap];0.96[EUR][1000 genomes]
rs4769673	0.87[EUR][1000 genomes]
rs4769679	1.00[GIH][hapmap]
rs60782582	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318626	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325000	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs74041703	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74045518	0.98[ASN][1000 genomes]
rs7984343	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9506076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9550433	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9551587	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9551588	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9551589	0.98[ASN][1000 genomes]
rs9551590	0.98[ASN][1000 genomes]
rs9551591	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9551592	1.00[ASN][1000 genomes]
rs9578069	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3406145	chr13:29616606-29917459	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Methotrexate phramacokinetics (acute lymphoblastic leukemia)	19901119	GWAS catalog

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29606200-29623600	Weak transcription	Aorta	Aorta
2	chr13:29612400-29633600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:29619200-29623200	Enhancers	Fetal Heart	heart
4	chr13:29620400-29620800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr13:29620400-29621000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:29620400-29621400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr13:29620400-29621400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr13:29620400-29621400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr13:29620600-29621000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr13:29620600-29621400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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